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bug fix for anisotropy data processing #45

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takashi310 wants to merge 2 commits into from
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bug fix for anisotropy data processing #45

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502646e
bug fix for anisotropy data processing
takashi310 Apr 4, 2025
9f0090a
Merge branch 'main' into fixfusion
takashi310 Sep 9, 2025
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21 changes: 16 additions & 5 deletions src/main/java/net/preibisch/bigstitcher/spark/SparkAffineFusion.java
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Original file line number Diff line number Diff line change
Expand Up @@ -273,6 +273,10 @@ else if ( outputPathURIString.toLowerCase().endsWith( ".h5" ) || outPathURI.toSt

final DataType dataType = driverVolumeWriter.getAttribute( "/", "Bigstitcher-Spark/DataType", DataType.class );

final long[] orig_bbMin = driverVolumeWriter.getAttribute( "/", "Bigstitcher-Spark/Boundingbox_min", long[].class );
if ( !Double.isNaN( anisotropyFactor ) )
orig_bbMin[ 2 ] = Math.round( Math.floor( orig_bbMin[ 2 ] * anisotropyFactor ) );

System.out.println( "FusionFormat: " + fusionFormat );
System.out.println( "FusionType: " + fusionType );
System.out.println( "Input XML: " + xmlURI );
Expand Down Expand Up @@ -329,8 +333,8 @@ else if (
{
System.out.println(
"The number of channels and timepoint in XML does not match the number in the export dataset."
+ "You have to specify which ViewIds/Channels/Illuminations/Tiles/Angles/Timepoints should be fused into"
+ "a specific 3D volume in the fusion dataset:");
+ "You have to specify which ViewIds/Channels/Illuminations/Tiles/Angles/Timepoints should be fused into"
+ "a specific 3D volume in the fusion dataset:");

viewIdsGlobal = AbstractSelectableViews.loadViewIds( dataGlobal, vi, angleIds, channelIds, illuminationIds, tileIds, timepointIds );

Expand Down Expand Up @@ -488,6 +492,13 @@ else if ( intensityN5PathURIString.toLowerCase().endsWith( ".h5" ) || intensityN
dataLocal.getViewRegistrations().getViewRegistrations(),
anisotropyFactor,
Double.NaN );

final HashMap< ViewId, AffineTransform3D > orig_registrations =
TransformVirtual.adjustAllTransforms(
viewIds,
dataLocal.getViewRegistrations().getViewRegistrations(),
Double.NaN,
Double.NaN );

final Converter conv;
final Type type;
Expand Down Expand Up @@ -518,7 +529,7 @@ else if ( dataType == DataType.UINT16 )
// The min coordinates of the block that this job renders (in pixels)
final int n = gridBlock[ 0 ].length;
final long[] superBlockOffset = new long[ n ];
Arrays.setAll( superBlockOffset, d -> gridBlock[ 0 ][ d ] + bbMin[ d ] );
Arrays.setAll( superBlockOffset, d -> gridBlock[ 0 ][ d ] + orig_bbMin[ d ] );

// The size of the block that this job renders (in pixels)
final long[] superBlockSize = gridBlock[ 1 ];
Expand All @@ -533,7 +544,7 @@ else if ( dataType == DataType.UINT16 )
Arrays.setAll( fusedBlockMax, d -> superBlockOffset[ d ] + superBlockSize[ d ] - 1 );

final List< ViewId > overlappingViews =
OverlappingViews.findOverlappingViews( dataLocal, viewIds, registrations, fusedBlock );
OverlappingViews.findOverlappingViews( dataLocal, viewIds, orig_registrations, fusedBlock );

if ( overlappingViews.size() == 0 )
return gridBlock;
Expand Down Expand Up @@ -808,4 +819,4 @@ public static void main(final String... args) throws SpimDataException {

System.exit(new CommandLine(new SparkAffineFusion()).execute(args));
}
}
}